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.gitattributes

@@ -0,0 +1,2 @@
+*.mcs filter=lfs diff=lfs merge=lfs -text
+*.mcs.gz filter=lfs diff=lfs merge=lfs -text

.gitea/workflows/build_and_test.yml

@@ -12,6 +12,7 @@ on:
 jobs:
   build-rpm:
     name: build:rpm (${{ matrix.distro }})
+    if: github.ref_type == 'tag'
     runs-on: ${{ matrix.runner }}
     strategy:
       fail-fast: false
@@ -20,48 +21,30 @@ jobs:
           - runner: jfjoch_rocky8
             distro: rocky8
             cmake_flags: -DJFJOCH_USE_CUDA=ON
-            pkg_glob: "*.rpm"
-            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12/upload
           - runner: jfjoch_rocky8
             distro: rocky8_sls9
             cmake_flags: -DJFJOCH_USE_CUDA=ON -DSLS9=ON
-            pkg_glob: "*.rpm"
-            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda12/upload
           - runner: jfjoch_rocky8
             distro: rocky8_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
-            pkg_glob: "*.rpm"
-            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda/upload
           - runner: jfjoch_rocky9
             distro: rocky9
             cmake_flags: -DJFJOCH_USE_CUDA=ON
-            pkg_glob: "*.rpm"
-            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-cuda13/upload
           - runner: jfjoch_rocky9
             distro: rocky9_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
-            pkg_glob: "*.rpm"
-            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-nocuda/upload
           - runner: jfjoch_ubuntu2204
             distro: ubuntu2204
             cmake_flags: -DJFJOCH_USE_CUDA=ON
-            pkg_glob: "*.deb"
-            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/cuda13/upload
           - runner: jfjoch_ubuntu2204
             distro: ubuntu2204_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
-            pkg_glob: "*.deb"
-            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/nocuda/upload
           - runner: jfjoch_ubuntu2404
             distro: ubuntu2404
             cmake_flags: -DJFJOCH_USE_CUDA=ON
-            pkg_glob: "*.deb"
-            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/noble/cuda13/upload
           - runner: jfjoch_ubuntu2404
             distro: ubuntu2404_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
-            pkg_glob: "*.deb"
-            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/noble/nocuda/upload
     steps:
       - uses: actions/checkout@v4
       - name: Build packages
@@ -75,21 +58,74 @@ jobs:
       - name: Upload packages
         if: github.ref_type == 'tag'
         shell: bash
-        env:
-          TOKEN: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}
         run: |
-          set -euo pipefail
           cd build
-          shopt -s nullglob
-          files=(${{ matrix.pkg_glob }})
-          if [ ${#files[@]} -eq 0 ]; then
-            echo "No package files found for pattern: ${{ matrix.pkg_glob }}"
-            exit 1
+          if [ "${{ matrix.distro }}" = "rocky8" ]; then
+            for file in *.rpm; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12/upload
+              fi
+            done
+          elif [ "${{ matrix.distro }}" = "rocky8_nocuda" ]; then
+            for file in *.rpm; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda/upload
+              fi
+            done
+          elif [ "${{ matrix.distro }}" = "rocky8_sls9" ]; then
+            for file in *.rpm; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda12/upload
+              fi
+            done
+          elif [ "${{ matrix.distro }}" = "rocky9_nocuda" ]; then
+            for file in *.rpm; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-nocuda/upload
+              fi
+            done
+          elif [ "${{ matrix.distro }}" = "ubuntu2204_nocuda" ]; then
+            for file in *.deb; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/nocuda/upload
+              fi
+            done
+          elif [ "${{ matrix.distro }}" = "ubuntu2204" ]; then
+            for file in *.deb; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/cuda13/upload
+              fi
+            done
+          elif [ "${{ matrix.distro }}" = "ubuntu2404" ]; then
+            for file in *.deb; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/debian/pool/noble/cuda13/upload
+              fi
+            done
+          fi
+          elif [ "${{ matrix.distro }}" = "ubuntu2404_nocuda" ]; then
+            for file in *.deb; do
+              if [ -f "$file" ]; then
+                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
+                     --upload-file "$file" \
+                     https://gitea.psi.ch/api/packages/mx/debian/pool/noble/nocuda/upload
+              fi
+            done
           fi
-          for file in "${files[@]}"; do
-            echo "Uploading $file -> ${{ matrix.upload_url }}"
-            curl --fail --user __token__:"$TOKEN" --upload-file "$file" "${{ matrix.upload_url }}"
-          done
   python-client:
     name: Generate python client
     runs-on: jfjoch_rocky8
@@ -103,7 +139,30 @@ jobs:
         run: |
           twine upload -u __token__ -p ${{ secrets.CI_PYPI_TOKEN }} --skip-existing dist/*
           twine upload -u __token__ -p ${{ secrets.PIP_REPOSITORY_API_TOKEN }} --repository-url https://gitea.psi.ch/api/packages/mx/pypi dist/*
-
+  create-release:
+    name: Create release
+    runs-on: jfjoch_rocky8
+    # if: github.ref_type == 'tag'
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: 'true' # Optional; should be the default
+      - name: Configure auth and fetch LFS
+        shell: bash
+        env:
+          GITEA_TOKEN: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}
+        run: |
+          git lfs install --local
+          AUTH=$(git config --local http.${{ github.server_url }}/.extraheader)
+          git config --local --unset http.${{ github.server_url }}/.extraheader
+          git config --local http.${{ github.server_url }}/${{ github.repository }}.git/info/lfs/objects/batch.extraheader "$AUTH"
+          git lfs pull
+      - name: Create release
+        env:
+          GITEA_TOKEN: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}
+        shell: bash
+        run: |
+          python3 gitea_create_release.py
   documentation:
     name: Build documentation
     runs-on: jfjoch_rocky8
@@ -133,6 +192,7 @@ jobs:
   unit-tests:
     name: Unit tests
     runs-on: jfjoch_rocky8
+    if: github.ref_type == 'tag'
     container:
       image: gitea.psi.ch/leonarski_f/jfjoch_rocky8:2509
       options: --gpus all

common/JFJochMessages.h

@@ -133,11 +133,9 @@ struct DataMessage {
     std::optional<int64_t> original_number;
     std::vector<Reflection> reflections;
 
-    std::vector<float> integration_B_logI;
-    std::vector<float> integration_B_one_over_d;
-
+    std::vector<float> integration_logI;
+    std::vector<float> integration_one_over_d;
     std::vector<float> integration_Isigma;
-    std::vector<float> integration_Isigma_one_over_d;
 
     std::optional<float> beam_corr_x;
     std::optional<float> beam_corr_y;

docker/rocky8/Dockerfile

@@ -14,6 +14,7 @@ RUN dnf -y update && \
       dnf-plugins-core \
       epel-release \
       git \
+      git-lfs \
       which \
       ca-certificates \
       wget \
@@ -60,12 +61,15 @@ RUN dnf -y update && \
       python3-pip \
       python3-setuptools \
       python3-wheel \
+      python3-requests \
       twine \
       openblas \
       openblas-devel \
       freetype-devel && \
     dnf clean all && rm -rf /var/cache/dnf
 
+RUN git lfs install
+
 RUN set -eux; \
     cd /tmp; \
     curl -LO https://www.openssl.org/source/openssl-${OPENSSL_VERSION}.tar.gz; \

docker/rocky9/Dockerfile

@@ -15,6 +15,7 @@ RUN dnf -y update && \
       dnf-plugins-core \
       epel-release \
       git \
+      git-lfs \
       which \
       ca-certificates \
       wget \
@@ -32,6 +33,7 @@ RUN dnf -y update && \
       redhat-rpm-config \
       ninja-build \
       python3 \
+      python3-requests \
       perl \
       pkgconf-pkg-config \
       libxcb-devel \
@@ -61,6 +63,8 @@ RUN dnf -y update && \
       freetype-devel && \
     dnf clean all && rm -rf /var/cache/dnf
 
+RUN git lfs install
+
 RUN set -eux; \
     cd /tmp; \
     curl -LO https://www.openssl.org/source/openssl-${OPENSSL_VERSION}.tar.gz; \

docs/CHANGELOG.md

@@ -1,11 +1,4 @@
 # Changelog
-## 1.0.0.rc.87
-This is an UNSTABLE release.
-
-* jfjoch_viewer: Display more image metadata (angle / exposure time)
-* jfjoch_viewer: Improve I/sigma and B-factor plots
-* jfjoch_broker: Estimate resolution based on visible spots
-
 ## 1.0.0.rc.86
 This is an UNSTABLE release.
 

gitea_create_release.py

@@ -0,0 +1,122 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+from typing import Optional
+try:
+    import requests
+except ModuleNotFoundError:
+    print("ERROR: Python 'requests' package is required. Please install it (e.g., pip install requests).")
+    sys.exit(1)
+
+gitea_api_url = "https://gitea.psi.ch/api/v1/"
+repo_owner = "mx"
+repo_name = "jungfraujoch"
+
+gitea_token = os.getenv('GITEA_TOKEN')
+if gitea_token is None:
+    print("ERROR: Required environment variables not set")
+    sys.exit(1)
+
+def read_version():
+    try:
+        with open('VERSION', 'r') as f:
+            return f.readline().strip()
+    except FileNotFoundError:
+        print("ERROR: VERSION file not found")
+        sys.exit(1)
+
+def create_release(version):
+    headers = {
+        'Authorization': f'token {gitea_token}',
+        'Content-Type': 'application/json',
+    }
+
+    data = {
+        'tag_name': version,
+        'name': f'Release {version}',
+        'draft': False,
+        'prerelease': '-rc.' in version or '-alpha.' in version or '-beta.' in version
+    }
+
+    url = f'{gitea_api_url}/repos/{repo_owner}/{repo_name}/releases'
+
+    response = requests.post(url, headers=headers, json=data)
+    if response.status_code != 201:
+        print(f"ERROR: Failed to create release. Status code: {response.status_code}")
+        print(response.text)
+        sys.exit(1)
+
+    release = response.json()
+    print(f"Successfully created release {version}")
+    return release
+
+def get_release_by_tag(version: str):
+    """
+    Fetch release information by tag name.
+    Returns the release object (dict) or exits on error.
+    """
+    headers = {
+        'Authorization': f'token {gitea_token}',
+        'Content-Type': 'application/json',
+    }
+    url = f'{gitea_api_url}/repos/{repo_owner}/{repo_name}/releases/tags/{version}'
+    resp = requests.get(url, headers=headers)
+    if resp.status_code != 200:
+        print(f"ERROR: Failed to fetch release {version}. Status code: {resp.status_code}")
+        print(resp.text)
+        sys.exit(1)
+    return resp.json()
+
+def upload_file_to_release(version: str, file_path: str, name: Optional[str] = None, label: Optional[str] = None):
+    """
+    Upload a file as an asset to the release identified by the given version tag.
+
+    :param version: Tag name of the release (e.g., '1.2.3' or '1.2.3-rc.1')
+    :param file_path: Local file path to upload
+    :param name: Optional asset name to display in release (defaults to filename)
+    :param label: Optional asset label (display name)
+    """
+    if not os.path.isfile(file_path):
+        print(f"ERROR: File not found: {file_path}")
+        sys.exit(1)
+
+    # Ensure the release exists and get its ID
+    release = get_release_by_tag(version)
+    release_id = release.get('id')
+    if release_id is None:
+        print("ERROR: Release ID not found in response")
+        sys.exit(1)
+
+    headers = {
+        'Authorization': f'token {gitea_token}',
+    }
+
+    asset_name = name if name else os.path.basename(file_path)
+    data = {'name': asset_name}
+    if label:
+        data['label'] = label
+
+    url = f'{gitea_api_url}/repos/{repo_owner}/{repo_name}/releases/{release_id}/assets'
+
+    with open(file_path, 'rb') as f:
+        files = {
+            'attachment': (asset_name, f, 'application/octet-stream'),
+        }
+        resp = requests.post(url, headers=headers, data=data, files=files)
+
+    if resp.status_code not in (201, 200):
+        print(f"ERROR: Failed to upload asset. Status code: {resp.status_code}")
+        print(resp.text)
+        sys.exit(1)
+
+    asset = resp.json()
+    browser_download_url = asset.get('browser_download_url') or asset.get('browser_url') or asset.get('url')
+    print(f"Uploaded asset '{asset_name}' to release {version}: {browser_download_url}")
+
+if __name__ == '__main__':
+    version = read_version()
+    release = create_release(version)
+
+    upload_file_to_release(version, 'fpga/images/jfjoch_fpga_pcie_8x10g.mcs.gz', 'jfjoch_fpga_pcie_8x10g.mcs.gz', '8x10G FPGA image')
+    upload_file_to_release(version, 'fpga/images/jfjoch_fpga_pcie_100g.mcs.gz', 'jfjoch_fpga_pcie_100g.mcs.gz', '100G FPGA image')

image_analysis/SpotAnalyze.cpp

@@ -8,7 +8,7 @@
 #include "spot_finding/StrongPixelSet.h"
 #include "bragg_integration/BraggIntegrate2D.h"
 #include "indexing/AnalyzeIndexing.h"
-#include "bragg_integration/CalcISigma.h"
+
 
 void SpotAnalyze(const DiffractionExperiment &experiment,
                  const SpotFindingSettings &spot_finding_settings,
@@ -86,13 +86,16 @@ void SpotAnalyze(const DiffractionExperiment &experiment,
                                                 ewald_dist_cutoff, output.number);
 
                     constexpr size_t kMaxReflections = 10000;
-                    if (res.size() > kMaxReflections) {
-                        output.reflections.assign(res.begin(), res.begin() + kMaxReflections);
+                    if (res.reflections.size() > kMaxReflections) {
+                        output.reflections.assign(res.reflections.begin(),
+                                                  res.reflections.begin() + kMaxReflections);
                     } else
-                        output.reflections = res;
+                        output.reflections = res.reflections;
 
-                    CalcISigma(output);
-                    CalcWilsonBFactor(output);
+                    output.b_factor = res.b_factor;
+                    output.integration_Isigma = res.Isigma;
+                    output.integration_logI = res.logI;
+                    output.integration_one_over_d = res.one_over_d;
                 }
             }
         }

image_analysis/bragg_integration/BraggIntegrate2D.cpp

@@ -4,10 +4,13 @@
 #include "BraggIntegrate2D.h"
 #include "BraggPrediction.h"
 
+#include "BraggIntegrationStats.h"
+
 template<class T>
 bool IntegrateReflection(Reflection &r, const T *image, size_t xpixel, size_t ypixel,
                          int64_t special_value, int64_t saturation,
                          float r_3, float r_1_sq, float r_2_sq, float r_3_sq) {
+
     r.I = 0;
     r.bkg = 0;
 
@@ -65,23 +68,24 @@ bool IntegrateReflection(Reflection &r, const T *image, size_t xpixel, size_t yp
 
 
 template<class T>
-std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experiment,
-                                          const CompressedImage &image,
-                                          const CrystalLattice &latt,
-                                          float dist_from_ewald_sphere,
-                                          int64_t special_value,
-                                          int64_t saturation,
-                                          int64_t image_number) {
+QuickIntegrateResult IntegrateInternal(const DiffractionExperiment &experiment,
+                                       const CompressedImage &image,
+                                       const CrystalLattice &latt,
+                                       float dist_from_ewald_sphere,
+                                       int64_t special_value,
+                                       int64_t saturation,
+                                       int64_t image_number) {
     auto settings = experiment.GetBraggIntegrationSettings();
     auto geom = experiment.GetDiffractionGeometry();
 
     auto start = std::chrono::high_resolution_clock::now();
     std::vector<uint8_t> buffer;
-    auto ptr = reinterpret_cast<const T *>(image.GetUncompressedPtr(buffer));
+    auto ptr = reinterpret_cast<const T*>(image.GetUncompressedPtr(buffer));
 
     auto refl = CalcBraggPredictions(experiment, latt, settings.GetDMinLimit_A(), dist_from_ewald_sphere);
 
-    std::vector<Reflection> ret;
+    QuickIntegrateResult ret;
+    BraggIntegrationStats stats(6.0, settings.GetDMinLimit_A(), 20); // Wilson statistics is only linear in certain resolution range
     float r_3 = settings.GetR3();
     float r_1_sq = settings.GetR1() * settings.GetR1();
     float r_2_sq = settings.GetR2() * settings.GetR2();
@@ -90,52 +94,51 @@ std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experimen
     for (const auto &[x, r_in]: refl) {
         Reflection r = r_in;
         if (IntegrateReflection(r, ptr, image.GetWidth(), image.GetHeight(), special_value, saturation,
-                                r_3, r_1_sq, r_2_sq, r_3_sq)) {
+                              r_3, r_1_sq, r_2_sq, r_3_sq)) {
             if (experiment.GetPolarizationFactor()) {
-                float pol = geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y,
-                                                           experiment.GetPolarizationFactor().value());
+                float pol = geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y, experiment.GetPolarizationFactor().value());
                 r.I /= pol;
                 r.bkg /= pol;
                 r.sigma /= pol;
             }
 
             r.image_number = static_cast<int>(image_number);
-            ret.push_back(r);
+            ret.reflections.push_back(r);
+            stats.AddReflection(r);
         }
     }
+    ret.b_factor = stats.BFactor();
+    ret.logI = stats.GetWilsonPlot();
+    ret.one_over_d = stats.GetWilsonPlotLegend();
+    ret.Isigma = stats.GetISigmaPlot();
 
     return ret;
 }
 
-std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
-                                         const CompressedImage &image,
-                                         const CrystalLattice &latt,
-                                         float dist_from_ewald_sphere,
-                                         int64_t image_number) {
+QuickIntegrateResult BraggIntegrate2D(const DiffractionExperiment &experiment,
+                                      const CompressedImage &image,
+                                      const CrystalLattice &latt,
+                                      float dist_from_ewald_sphere,
+                                      int64_t image_number) {
     if (image.GetCompressedSize() == 0)
         return {};
 
     switch (image.GetMode()) {
         case CompressedImageMode::Int8:
-            return IntegrateInternal<int8_t>(experiment, image, latt, dist_from_ewald_sphere, INT8_MIN, INT8_MAX,
-                                             image_number);
+            return IntegrateInternal<int8_t>(experiment, image, latt, dist_from_ewald_sphere, INT8_MIN, INT8_MAX, image_number);
         case CompressedImageMode::Int16:
-            return IntegrateInternal<int16_t>(experiment, image, latt, dist_from_ewald_sphere, INT16_MIN, INT16_MAX,
-                                              image_number);
+            return IntegrateInternal<int16_t>(experiment, image, latt, dist_from_ewald_sphere, INT16_MIN, INT16_MAX, image_number);
         case CompressedImageMode::Int32:
-            return IntegrateInternal<int32_t>(experiment, image, latt, dist_from_ewald_sphere, INT32_MIN, INT32_MAX,
-                                              image_number);
+            return IntegrateInternal<int32_t>(experiment, image, latt, dist_from_ewald_sphere, INT32_MIN, INT32_MAX, image_number);
         case CompressedImageMode::Uint8:
-            return IntegrateInternal<uint8_t>(experiment, image, latt, dist_from_ewald_sphere, UINT8_MAX, UINT8_MAX,
-                                              image_number);
+            return IntegrateInternal<uint8_t>(experiment, image, latt, dist_from_ewald_sphere, UINT8_MAX, UINT8_MAX, image_number);
         case CompressedImageMode::Uint16:
-            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT16_MAX, UINT16_MAX,
-                                               image_number);
+            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT16_MAX, UINT16_MAX, image_number);
         case CompressedImageMode::Uint32:
-            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT32_MAX, UINT32_MAX,
-                                               image_number);
+            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT32_MAX, UINT32_MAX, image_number);
         default:
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                   "Image mode not supported");
     }
 }
+

image_analysis/bragg_integration/BraggIntegrate2D.h

@@ -9,10 +9,18 @@
 #include "../../common/CrystalLattice.h"
 #include "../../common/Reflection.h"
 
-std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
-                                         const CompressedImage &image,
-                                         const CrystalLattice &latt,
-                                         float dist_from_ewald_sphere,
-                                         int64_t image_number);
+struct QuickIntegrateResult {
+    std::vector<Reflection> reflections;
+    std::optional<float> b_factor;
+    std::vector<float> logI;
+    std::vector<float> one_over_d;
+    std::vector<float> Isigma;
+};
+
+QuickIntegrateResult BraggIntegrate2D(const DiffractionExperiment &experiment,
+                                      const CompressedImage &image,
+                                      const CrystalLattice &latt,
+                                      float dist_from_ewald_sphere,
+                                      int64_t image_number);
 
 #endif //JFJOCH_BRAGGINTEGRATE2D_H

image_analysis/bragg_integration/BraggIntegrationStats.cpp

@@ -39,12 +39,12 @@ std::optional<float> BraggIntegrationStats::BFactor() {
                            + (static_cast<float>(i) + 0.5) * (one_over_dmin - one_over_dmax) / static_cast<float>(nshells);
         wilson_plot_legend.push_back(one_over_d);
         if (count[i] == 0 )
-            plot_Isigma.push_back(0);
+            plot_Isigma.push_back(NAN);
         else
             plot_Isigma.push_back(I_sigma[i] / count[i]);
 
         if (count[i] == 0 || I[i] < 0.0 || I_sigma[i] < 0.2f * count[i])
-            wilson_plot.push_back(0);
+            wilson_plot.push_back(NAN);
         else
             wilson_plot.push_back(log(I[i] / count[i]));
     }
@@ -60,7 +60,7 @@ std::vector<float> BraggIntegrationStats::GetWilsonPlot() {
     return wilson_plot;
 }
 
-std::vector<float> BraggIntegrationStats::GetOneOverDPlot() {
+std::vector<float> BraggIntegrationStats::GetWilsonPlotLegend() {
     return wilson_plot_legend;
 }
 

image_analysis/bragg_integration/BraggIntegrationStats.h

@@ -23,11 +23,11 @@ class BraggIntegrationStats {
     std::vector<float> wilson_plot_legend;
     std::vector<float> plot_Isigma;
 public:
-    explicit BraggIntegrationStats(float d_max_A, float d_min_A, int32_t nshells);
+    explicit BraggIntegrationStats(float d_max_A = 6.0, float d_min_A = 1.5, int32_t nshells = 20);
     void AddReflection(const Reflection &r);
     std::optional<float> BFactor();
     std::vector<float> GetWilsonPlot();
-    std::vector<float> GetOneOverDPlot();
+    std::vector<float> GetWilsonPlotLegend();
     std::vector<float> GetISigmaPlot();
 };
 

image_analysis/bragg_integration/CMakeLists.txt

@@ -6,8 +6,6 @@ ADD_LIBRARY(JFJochBraggIntegration STATIC
         BraggIntegrationStats.cpp
         BraggIntegrationStats.h
         Regression.h
-        CalcISigma.cpp
-        CalcISigma.h
 )
 
 TARGET_LINK_LIBRARIES(JFJochBraggIntegration JFJochCommon)

image_analysis/bragg_integration/CalcISigma.cpp

@@ -1,32 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include "CalcISigma.h"
-#include "BraggIntegrationStats.h"
-
-void CalcISigma(DataMessage &msg) {
-    if (msg.reflections.empty())
-        return;
-
-    BraggIntegrationStats stats(50.0, 1.5, 20);
-    for (const auto &r: msg.reflections)
-        stats.AddReflection(r);
-
-    stats.BFactor(); // need to do it to generate plots...
-
-    msg.integration_Isigma = stats.GetISigmaPlot();
-    msg.integration_Isigma_one_over_d = stats.GetOneOverDPlot();
-}
-
-void CalcWilsonBFactor(DataMessage &msg) {
-    if (msg.reflections.empty())
-        return;
-
-    BraggIntegrationStats stats(6.0, 3.0, 10); // Wilson statistics is only linear in certain resolution range
-    for (const auto &r: msg.reflections)
-        stats.AddReflection(r);
-
-    msg.b_factor = stats.BFactor();
-    msg.integration_B_logI = stats.GetWilsonPlot();
-    msg.integration_B_one_over_d = stats.GetOneOverDPlot();
-}

image_analysis/bragg_integration/CalcISigma.h

@@ -1,12 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#ifndef JFJOCH_CALCISIGMA_H
-#define JFJOCH_CALCISIGMA_H
-
-#include "../../common/JFJochMessages.h"
-
-void CalcISigma(DataMessage &msg);
-void CalcWilsonBFactor(DataMessage &msg);
-
-#endif //JFJOCH_CALCISIGMA_H

image_analysis/spot_finding/SpotFindingSettings.h

@@ -19,7 +19,7 @@ struct SpotFindingSettings {
     float ice_ring_width_Q_recipA = 0.02;
 
     bool indexing = true;
-    bool quick_integration = true;
+    bool quick_integration = false;
 };
 
 #endif //JUNGFRAUJOCH_SPOTFINDINGSETTINGS_H

reader/JFJochHDF5Reader.cpp

@@ -4,7 +4,6 @@
 #include "JFJochHDF5Reader.h"
 #include "spdlog/fmt/fmt.h"
 #include "../image_analysis/bragg_integration/BraggIntegrationStats.h"
-#include "../image_analysis/bragg_integration/CalcISigma.h"
 
 std::vector<hsize_t> GetDimension(HDF5Object& object, const std::string& path) {
     const auto dim = object.GetDimension(path);
@@ -543,6 +542,8 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
             || h.size() != predicted_x.size() || h.size() != predicted_y.size()
             || h.size() != int_sum.size() || h.size() != int_err.size() || h.size() != bkg.size())
             throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of reflections dataset");
+        BraggIntegrationSettings settings;
+        BraggIntegrationStats stats(6.0, settings.GetDMinLimit_A(), 10); // Wilson statistics is only linear in certain resolution range
 
         for (size_t i = 0; i < h.size(); i++) {
             Reflection r{
@@ -556,10 +557,13 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
                 .bkg = bkg.at(i),
                 .sigma = int_err.at(i)
             };
+            stats.AddReflection(r);
             message.reflections.emplace_back(r);
         }
-        CalcISigma(message);
-        CalcWilsonBFactor(message);
+
+        message.integration_logI = stats.GetWilsonPlot();
+        message.integration_one_over_d = stats.GetWilsonPlotLegend();
+        message.integration_Isigma = stats.GetISigmaPlot();
     }
 
     return true;

reader/JFJochHttpReader.cpp

@@ -8,7 +8,6 @@
 #include "../frame_serialize/CBORStream2Deserializer.h"
 #include "../broker/gen/model/Image_buffer_status.h"
 #include "../broker/gen/model/Plots.h"
-#include "../image_analysis/bragg_integration/CalcISigma.h"
 
 void JFJochHttpReader::Close_i() {
     addr = "";
@@ -156,10 +155,6 @@ bool JFJochHttpReader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
             return false;
 
         message = *msg->data_message;
-
-        CalcISigma(message);
-        CalcWilsonBFactor(message);
-
         return true;
     } catch (std::exception &e) {
         return false;

viewer/JFJochViewerImageStatistics.cpp

@@ -3,7 +3,6 @@
 
 #include "JFJochViewerImageStatistics.h"
 #include <QFormLayout>
-#include <QRegularExpression>
 
 static QString mkSourceInstrumentText(const DiffractionExperiment& exp) {
     QString src, inst;
@@ -62,11 +61,11 @@ JFJochViewerImageStatistics::JFJochViewerImageStatistics(QWidget *parent) : QWid
     sample_name = new QLabel(this);
     layout->addRow("Sample:", sample_name);
 
-    exposure_time = new QLabel(this);
-    layout->addRow(new QLabel("Exposure Time:"), exposure_time);
+    error_pixels = new QLabel(this);
+    layout->addRow(new QLabel("Error pixels:"), error_pixels);
 
-    rotation_angle = new QLabel(this);
-    layout->addRow(new QLabel("Image angle:"), rotation_angle);
+    sat_pixels = new QLabel(this);
+    layout->addRow(new QLabel("Sat. pixels:"), sat_pixels);
 
     valid_values = new QLabel(this);
     layout->addRow(new QLabel("Valid values:"), valid_values);
@@ -100,17 +99,6 @@ JFJochViewerImageStatistics::JFJochViewerImageStatistics(QWidget *parent) : QWid
 
 }
 
-QString TrimZeros(double number, int precision) {
-    auto s = QString::number(number, 'f', precision);
-    s.remove(QRegularExpression("\\.?0+$"));
-    if (s.isEmpty()) s = "0";
-    return s;
-}
-
-QString FormatTime(std::chrono::microseconds time) {
-    return TrimZeros(time.count()/1e6, 6);
-}
-
 void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
     if (!image) {
         source_name->setText("");
@@ -119,12 +107,9 @@ void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderIm
         dataset_name->setToolTip("");
         detector_name->setText("");
         detector_name->setToolTip("");
-        exposure_time->setText("");
-        exposure_time->setToolTip("");
-        rotation_angle->setText("");
-        rotation_angle->setToolTip("");
+        error_pixels->setText("");
+        sat_pixels->setText("");
         valid_values->setText("");
-        valid_values->setToolTip("");
         spots->setText("");
         bkg_estimate->setText("");
         indexed->setText("");
@@ -161,24 +146,16 @@ void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderIm
     detector_name->setText(text);
 
     source_name->setText(mkSourceInstrumentText(exp));
-    source_name->setToolTip(mkSourceInstrumentTooltip(exp));
+    source_name->setToolTip(mkSampleTooltip(exp));
 
     sample_name->setText(mkSampleText(exp));
     sample_name->setToolTip(mkSampleTooltip(exp));
 
-    if (exp.GetGoniometer()) {
-        rotation_angle->setText(QString("<b>%1°</b>")
-            .arg(TrimZeros(exp.GetGoniometer()->GetIncrement_deg(), 3)));
-        rotation_angle->setToolTip(QString("Start angle: <b>%1°</b><br/>This image: <b>%2°</b>")
-            .arg(TrimZeros(exp.GetGoniometer()->GetStart_deg(), 3))
-            .arg(TrimZeros(exp.GetGoniometer()->GetAngle_deg(image->ImageData().number), 3))
-            );
-    } else {
-        rotation_angle->setText(QString("-"));
-        rotation_angle->setToolTip("");
-    }
-    exposure_time->setText(QString("<b>%1</b> s").arg(FormatTime(exp.GetImageTime())));
-    exposure_time->setToolTip(QString("Count time: <b>%1</b> s<br/>").arg(FormatTime(exp.GetImageCountTime())));
+    text = QString("<b>%1</b>").arg(image->ErrorPixels().size());
+    error_pixels->setText(text);
+
+    text = QString("<b>%1</b>").arg(image->SaturatedPixels().size());
+    sat_pixels->setText(text);
 
     text = QString("<b>%1</b>").arg(image->ImageData().spots.size());
     spots->setText(text);
@@ -193,8 +170,6 @@ void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderIm
             .arg(image->ValidPixels().begin()->first)
             .arg(image->ValidPixels().rbegin()->first);
     valid_values->setText(text);
-    valid_values->setToolTip(QString("Error pixels: <b>%1</b><br/>Saturated pixels: <b>%2</b>")
-        .arg(image->ErrorPixels().size()).arg(image->SaturatedPixels().size()));
 
     if (!image->Dataset().bkg_estimate.empty()) {
         text = QString("<b>%1</b>").arg(image->ImageData().bkg_estimate.value_or(0));

viewer/JFJochViewerImageStatistics.h

@@ -15,8 +15,8 @@ class JFJochViewerImageStatistics : public QWidget {
     QLabel *sample_name;
     QLabel *dataset_name;
     QLabel *detector_name;
-    QLabel *exposure_time;
-    QLabel *rotation_angle;
+    QLabel *error_pixels;
+    QLabel *sat_pixels;
     QLabel *spots;
     QLabel *valid_values;
     QLabel *indexed;

viewer/JFJochViewerSidePanelChart.cpp

@@ -24,8 +24,8 @@ JFJochViewerSidePanelChart::JFJochViewerSidePanelChart(QWidget *parent) : QWidge
     azint_image = new JFJochAzIntImageView(this);
 
     stack = new QStackedWidget(this);
-    stack->addWidget(azint_plot); // index 0
-    stack->addWidget(azint_image); // index 1
+    stack->addWidget(azint_plot);   // index 0
+    stack->addWidget(azint_image);  // index 1
     layout->addWidget(stack);
 
     setLayout(layout);
@@ -44,8 +44,7 @@ void JFJochViewerSidePanelChart::comboBoxSelected(int val) {
 }
 
 void JFJochViewerSidePanelChart::redrawPlot() {
-    std::vector<float> x, y;
-    bool one_over_x = false;
+    std::vector<float> x,y;
     if (image) {
         auto index = combo_box->currentIndex();
         switch (combo_box->itemData(index).toInt()) {
@@ -54,14 +53,12 @@ void JFJochViewerSidePanelChart::redrawPlot() {
                 y = image->GetAzInt1D();
                 break;
             case 1:
-                x = image->ImageData().integration_B_one_over_d;
-                y = image->ImageData().integration_B_logI;
-                one_over_x = true;
+                x = image->ImageData().integration_one_over_d;
+                y = image->ImageData().integration_logI;
                 break;
             case 2:
-                x = image->ImageData().integration_Isigma_one_over_d;
+                x = image->ImageData().integration_one_over_d;
                 y = image->ImageData().integration_Isigma;
-                one_over_x = true;
                 break;
             case 4:
                 x = image->Dataset().experiment.GetFluorescenceSpectrum().GetEnergy_eV();
@@ -86,7 +83,7 @@ void JFJochViewerSidePanelChart::redrawPlot() {
         }
     }
     if (!x.empty() && !y.empty()) {
-        azint_plot->UpdateData(x, y, one_over_x);
+        azint_plot->UpdateData(x,y);
     } else {
         azint_plot->ClearData();
     }
@@ -95,4 +92,4 @@ void JFJochViewerSidePanelChart::redrawPlot() {
 void JFJochViewerSidePanelChart::loadImage(std::shared_ptr<const JFJochReaderImage> in_image) {
     image = in_image;
     redrawPlot();
-}
+}

viewer/widgets/JFJochSimpleChartView.cpp

@@ -6,7 +6,6 @@
 #include <QMenu>
 #include <QClipboard>
 #include <QApplication>
-#include <QCategoryAxis>
 
 JFJochSimpleChartView::JFJochSimpleChartView(QWidget *parent)
         : QChartView(new QChart(), parent) {
@@ -16,58 +15,16 @@ JFJochSimpleChartView::JFJochSimpleChartView(QWidget *parent)
     //setRubberBand(QChartView::RubberBand::HorizontalRubberBand);
 }
 
-void JFJochSimpleChartView::UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y, bool one_over_x) {
-    x = in_x; y = in_y;
+void JFJochSimpleChartView::UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y) {
+    x = in_x;
+    y = in_y;
     chart()->removeAllSeries();
-    // Remove all axes to avoid duplicates
-    for (auto ax : chart()->axes()) chart()->removeAxis(ax);
-
-    if (x.empty() || x.size() != y.size()) return;
-
-    auto* series = new QLineSeries(this);
-    for (size_t i = 0; i < x.size(); ++i) series->append(x[i], y[i]);
-    chart()->addSeries(series);
-
-    auto* axY = new QValueAxis();
-    chart()->addAxis(axY, Qt::AlignLeft);
-    series->attachAxis(axY);
-
-    // Build X range
-    auto [minXIt, maxXIt] = std::minmax_element(x.begin(), x.end());
-    const double xmin = *minXIt, xmax = *maxXIt;
-
-    if (one_over_x) {
-        // Hidden X value axis on top for grid/range
-        auto* axXTop = new QValueAxis();
-        axXTop->setRange(xmin, xmax);
-        axXTop->setTickCount(5);
-        axXTop->setLabelsVisible(false);
-        chart()->addAxis(axXTop, Qt::AlignTop);
-        series->attachAxis(axXTop);
-
-        // Visible category axis at bottom for 1/x labels
-        auto* axXcat = new QCategoryAxis();
-        axXcat->setLabelsPosition(QCategoryAxis::AxisLabelsPositionOnValue);
-        axXcat->setGridLineVisible(false);
-        axXcat->setMinorGridLineVisible(false);
-
-        const int tickCount = axXTop->tickCount();
-        const double step = (tickCount > 1) ? (xmax - xmin) / (tickCount - 1) : 0.0;
-        for (int i = 0; i < tickCount; ++i) {
-            const double xv = xmin + i * step;
-            const QString lab = (std::abs(xv) < 1e-12)
-                                ? QStringLiteral("∞")
-                                : QString::number(1.0 / xv, 'g', 4);
-            axXcat->append(lab, xv);
-        }
-        chart()->addAxis(axXcat, Qt::AlignBottom);
-        series->attachAxis(axXcat);
-    } else {
-        // Normal value axis at bottom
-        auto* axX = new QValueAxis();
-        axX->setRange(xmin, xmax);
-        chart()->addAxis(axX, Qt::AlignBottom);
-        series->attachAxis(axX);
+    if (!x.empty() && x.size() == y.size()) {
+        series = new QLineSeries(this);
+        for (int i = 0; i < x.size(); i++)
+            series->append(x[i], in_y[i]);
+        chart()->addSeries(series);
+        chart()->createDefaultAxes();
     }
 }
 
@@ -94,31 +51,3 @@ void JFJochSimpleChartView::contextMenuEvent(QContextMenuEvent *event) {
         cb->setText(out);
     }
 }
-
-void JFJochSimpleChartView::applyInverseXLabels(QValueAxis* axX, QLineSeries* s) {
-    axX->setTickCount(5); // adjust as needed
-    axX->setLabelsVisible(false); // hide default numeric labels
-
-    auto* axXcat = new QCategoryAxis();
-    axXcat->setLabelsPosition(QCategoryAxis::AxisLabelsPositionOnValue);
-    axXcat->setGridLineVisible(false);
-    axXcat->setMinorGridLineVisible(false);
-
-    const int tickCount = axX->tickCount();
-    const double min = axX->min();
-    const double max = axX->max();
-    const double step = (tickCount > 1) ? (max - min) / (tickCount - 1) : 0.0;
-
-    for (int i = 0; i < tickCount; ++i) {
-        const double xv = min + i * step;
-        if (std::abs(xv) < 1e-12) {
-            axXcat->append("∞", xv);
-        } else {
-            const double inv = 1.0 / xv;
-            axXcat->append(QString::number(inv, 'g', 4), xv);
-        }
-    }
-
-    chart()->addAxis(axXcat, Qt::AlignBottom);
-    s->attachAxis(axXcat);
-}

viewer/widgets/JFJochSimpleChartView.h

@@ -11,16 +11,15 @@
 class JFJochSimpleChartView  : public QChartView {
     Q_OBJECT
 
+    QLineSeries *series = nullptr;
     std::vector<float> x, y;
 
-    void applyInverseXLabels(QValueAxis* axX, QLineSeries* s);
     void Plot();
 protected:
     void contextMenuEvent(QContextMenuEvent *event) override;
 public:
     JFJochSimpleChartView(QWidget *parent = nullptr);
-    void UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y, bool one_over_x);
-
+    void UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y);
     void ClearData();
 };